The DOI matches its Crossref record; 41 of the 41 references it cites were found in a registry or an index.
These aren’t the loci you’e looking for: Principles of effective SNP filtering for molecular ecologists
Open accessAbstract
Sequencing reduced‐representation libraries of restriction site‐associated DNA (RAD seq) to identify single nucleotide polymorphisms (SNP s) is quickly becoming a standard methodology for molecular ecologists. Because of the scale of RAD seq data sets, putative loci cannot be assessed individually, making the process of filtering noise and correctly identifying biologically meaningful signal more difficult. Artefacts introduced during library preparation and/or bioinformatic processing of SNP data can create patterns that are incorrectly interpreted as indicative of population structure or natural selection. Therefore, it is crucial to carefully consider types of errors that may be introduced during laboratory work and data processing, and how to minimize, detect and remove these errors. Here, we discuss issues inherent to RAD seq methodologies that can result in artefacts during library preparation and locus reconstruction resulting in erroneous SNP calls and, ultimately, genotyping error. Further, we describe steps that can be implemented to create a rigorously filtered data set consisting of markers accurately representing independent loci and compare the effect of different combinations of filters on four RAD data sets. At last, we stress the importance of publishing raw sequence data along with final filtered data sets in addition to detailed documentation of filtering steps and quality control measures.
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Cites
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A framework for variation discovery and genotyping using next-generation DNA sequencing data
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A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species
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Stacks: an analysis tool set for population genomics
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Haplotype-based variant detection from short-read sequencing
Garrison, E., & Marth, G. (2012) · arXiv · doi:10.48550/arxiv.1207.3907 · Cited by 3,700
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Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers
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Reproducible research in computational science
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“Nevertheless, it is incumbent upon the authors to document data preparation and quality control steps and make these available to the scientific community along with raw data sets to ensure that data analyses are transparent and fully reproducible (Leek & Peng 2015; Peng 2014).”
BackgroundRARE ALLELES AS INDICATORS OF GENE FLOW
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Cited by
Conservation and the Genomics of Populations
Allendorf, F. W., Funk, W. C., Aitken, S. N., Byrne, M., Luikart, G., & Antunes, A. (2022) · doi:10.1093/oso/9780198856566.001.0001 · Cited by 207
Next-generation data filtering in the genomics era
Hemstrom, W., Grummer, J. A., Luikart, G., & Christie, M. R. (2024) · Nature Reviews Genetics · doi:10.1038/s41576-024-00738-6 · Cited by 77
Highly replicated evolution of parapatric ecotypes
James, M. E., Arenas-Castro, H., Groh, J. S., Allen, S. L., Engelstädter, J., & Ortiz-Barrientos, D. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab207 · Cited by 30
Metadata
- Authors
- O'Leary, S. J., Puritz, J. B., Willis, S. C., Hollenbeck, C. M., & Portnoy, D. S.
- Venue
- Molecular Ecology
- Publisher
- Wiley
- Published
- 2018-07-27
- Volume
- 27
- Issue
- 16
- Pages
- 3193-3206
- ISSN
- 0962-1083 (ISSN-L)
- 1365-294X
- OpenAlex
- W2833129587
- Cited by
- 434
- References
- 41
- FWCI
- 17.49
- Type
- journal article
- Language
- en
- Open access
- green
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